Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012016.1 Corchorus capsularis cultivar CVL-1 contig12037, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24298
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:5883 original size:57 final size:57
Alignment explanation
Indices: 5811--5988 Score: 223
Period size: 57 Copynumber: 3.0 Consensus size: 57
5801 AGAGATTTAA
*
5811 ATTTCTCTTCCAAATATGTGTATTCATACTTCTTATGTGGTATCAGAGCCAGGGTTT
1 ATTTCTCTTCCAAATATGTGTATTCATACTTCTTATATGGTATCAGAGCCAGGGTTT
* * **
5868 ATTTATCTTCCAAATATGTGTATTCATACTTCTTATATGTGTCTCA-ATACAGAGAGATTT
1 ATTTCTCTTCCAAATATGTGTATTCATACTTCTTATATG-GTATCAGAGCCAG-G-G-TTT
* * *
5928 AAATTTCTCTTCCAAATATGTGTATTCATGCTTCTTATTTGGTATCAGAGCCAGGATTT
1 --ATTTCTCTTCCAAATATGTGTATTCATACTTCTTATATGGTATCAGAGCCAGGGTTT
5987 AT
1 AT
5989 CTCATCTCCC
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
57 43 0.42
58 6 0.06
59 4 0.04
60 3 0.03
61 6 0.06
62 40 0.39
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (57 bp):
ATTTCTCTTCCAAATATGTGTATTCATACTTCTTATATGGTATCAGAGCCAGGGTTT
Found at i:11934 original size:4 final size:4
Alignment explanation
Indices: 11925--11954 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
11915 TGATACAAAT
11925 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
11955 CCTTTGCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:14697 original size:10 final size:10
Alignment explanation
Indices: 14682--14714 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
14672 ATCTTAATTG
14682 AATATATATA
1 AATATATATA
14692 AATATATATA
1 AATATATATA
*
14702 TATATATATA
1 AATATATATA
14712 AAT
1 AAT
14715 GAAGAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATATATA
Found at i:15286 original size:23 final size:22
Alignment explanation
Indices: 15243--15286 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15233 AATACAAATA
* *
15243 TAAAAAAGAAAAAAGTATGATT
1 TAAAAAAAAAAAAACTATGATT
15265 TAAAAAAAAAAAAACTACTGAT
1 TAAAAAAAAAAAAACTA-TGAT
15287 AAAATGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (22 bp):
TAAAAAAAAAAAAACTATGATT
Found at i:18468 original size:15 final size:14
Alignment explanation
Indices: 18417--18509 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
18407 TTATGATTAG
*
18417 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
18431 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
18444 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
18457 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
18470 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
18483 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
18496 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
18509 T
1 T
18510 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:18477 original size:26 final size:26
Alignment explanation
Indices: 18448--18515 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
18438 TACTTAGTTT
18448 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
18474 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
18500 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
18516 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:18561 original size:24 final size:25
Alignment explanation
Indices: 18524--18582 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
18514 AAAATGAAGG
*
18524 AAATGAA-TTTGAAG-ATTTGTTAA
1 AAATGAAGTTTGAAGAAGTTGTTAA
18547 AAATGAAGTTTGAAGAAGTTGTTAA
1 AAATGAAGTTTGAAGAAGTTGTTAA
*
18572 AAATTAAGTTT
1 AAATGAAGTTT
18583 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAA
Found at i:18695 original size:21 final size:22
Alignment explanation
Indices: 18653--18697 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
18643 CAACAGTGTA
**
18653 AAAAGAGGGGGCAGTATTTAGC
1 AAAAGAGGGGGCAGTAAATAGC
*
18675 AAAAG-GGGGGCGGTAAATAGC
1 AAAAGAGGGGGCAGTAAATAGC
18696 AA
1 AA
18698 TCCAGATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.09, G:0.38, T:0.13
Consensus pattern (22 bp):
AAAAGAGGGGGCAGTAAATAGC
Found at i:18963 original size:2 final size:2
Alignment explanation
Indices: 18950--19001 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
18940 AGTATATCAA
* *
18950 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT GT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18990 AT AT AT GT AT AT
1 AT AT AT AT AT AT
19002 TATTAATTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19390 original size:22 final size:22
Alignment explanation
Indices: 19350--19396 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19340 AAAAGAGCTT
* * *
19350 AATTCAAGTCATGAGATAAATA
1 AATTCAAATCATGAAATAAAAA
*
19372 AATTCAAATCATTAAATAAAAA
1 AATTCAAATCATGAAATAAAAA
19394 AAT
1 AAT
19397 GTAATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (22 bp):
AATTCAAATCATGAAATAAAAA
Found at i:20437 original size:11 final size:11
Alignment explanation
Indices: 20412--20452 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
20402 CCCTTTTCTA
20412 TATAAAATAAAT
1 TATAAAAT-AAT
*
20424 TATCAAATAAT
1 TATAAAATAAT
20435 TATAAAATTAAT
1 TATAAAA-TAAT
20447 TATAAA
1 TATAAA
20453 CTAGAATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:21605 original size:22 final size:22
Alignment explanation
Indices: 21535--21628 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 22
21525 TGTCTTTGTC
** *
21535 AAATTTTGATAATTAAACTATG
1 AAATTTTGATAACCACACTATG
*
21557 AAATTTTGATAACCACACAATG
1 AAATTTTGATAACCACACTATG
* * * *
21579 GAATTTTGTTAACCTCCCTATG
1 AAATTTTGATAACCACACTATG
* ** *
21601 AAATTTTAATAGTCACACTACG
1 AAATTTTGATAACCACACTATG
21623 AAATTT
1 AAATTT
21629 CAAAATTTTT
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:22642 original size:22 final size:22
Alignment explanation
Indices: 22591--23273 Score: 213
Period size: 22 Copynumber: 30.9 Consensus size: 22
22581 AATAGTACCA
* * *
22591 CACTATAAAATTTTAATAATCT
1 CACTATGAAATTTTGATAACCT
* *
22613 AAATATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
* * * ***
22635 CCCCATGAAATTTCGATATTGT
1 CACTATGAAATTTTGATAACCT
* * * *
22657 CCCTATAAAATTTTAATAACCA
1 CACTATGAAATTTTGATAACCT
*
22679 CACTATGAAATTTTGATAACGT
1 CACTATGAAATTTTGATAACCT
** * *
22701 CTGTATGAAATTTTGGTAA-GT
1 CACTATGAAATTTTGATAACCT
22722 ACACTATGAAATTTTGATAACCT
1 -CACTATGAAATTTTGATAACCT
* * * **
22745 CTCTACGAAATTTCGATTGCCT
1 CACTATGAAATTTTGATAACCT
* * **
22767 C-CTTACG-AAGTTTGATTTCCT
1 CAC-TATGAAATTTTGATAACCT
*
22788 C-TTGATGAAATTTTGATAA-CT
1 CACT-ATGAAATTTTGATAACCT
*
22809 ACACTAT-AAATTTT-AGTAACATT
1 -CACTATGAAATTTTGA-TAAC-CT
22832 C-CTATGAAATTTT-ATTAA--T
1 CACTATGAAATTTTGA-TAACCT
* * *
22851 CTCTATGAAATTTTAATATCACAAT
1 CACTATGAAATTTTGATA--AC-CT
* * *
22876 -ATATATAAAAATTTTTGGTAACC-
1 CA-CTAT-GAAA-TTTTGATAACCT
* *
22899 AACCTATGAAATTTTGGTAACCT
1 CA-CTATGAAATTTTGATAACCT
* * *
22922 C-CGTATGAAATTGTGGTAATCTT
1 CAC-TATGAAATTTTGATAA-CCT
*
22945 CAC-ATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCT
* *
22966 CATTATGAAATTTTGATAACTTT
1 CACTATGAAATTTTGATAAC-CT
* * *
22989 C-TTATGAAACTTTGATTATATCT
1 CACTATGAAATTTTGA-TA-ACCT
* *
23012 -TCTCATGAAATTTTGATAACCA
1 CACT-ATGAAATTTTGATAACCT
* *
23034 CACCAT-AAAATTTGAATAACGC-
1 CACTATGAAATTTTG-ATAAC-CT
* *
23056 CTCTATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCT
*
23078 CAC--TGAAATTTTAATAACCT
1 CACTATGAAATTTTGATAACCT
* * *
23098 -TCTAATG-AATTTCGGTAA-CT
1 CACT-ATGAAATTTTGATAACCT
**
23118 ACACTATGAAATTTTGATAATTGT
1 -CACTATGAAATTTTGATAA-CCT
23142 C-CTATGAAATTTTTG-TAA--T
1 CACTATGAAA-TTTTGATAACCT
* * *
23161 CATATCATGAAATTTTGACAACCA
1 CA-CT-ATGAAATTTTGATAACCT
* * *
23185 CACTGTGAAATTGTGATAACTTT
1 CACTATGAAATTTTGATAAC-CT
* **
23208 C-TTATGAAATTTTGATAATAT
1 CACTATGAAATTTTGATAACCT
*
23229 -GCTATGAAATTTTGATAA-CT
1 CACTATGAAATTTTGATAACCT
23249 ACACTACGGATGAAATTTTGATAAC
1 -CACT----ATGAAATTTTGATAAC
23274 TACACGGAAA
Statistics
Matches: 491, Mismatches: 109, Indels: 117
0.68 0.15 0.16
Matches are distributed among these distances:
19 5 0.01
20 34 0.07
21 80 0.16
22 289 0.59
23 33 0.07
24 20 0.04
25 6 0.01
26 18 0.04
27 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:22712 original size:44 final size:44
Alignment explanation
Indices: 22616--23273 Score: 252
Period size: 44 Copynumber: 14.9 Consensus size: 44
22606 ATAATCTAAA
* * * * ** *
22616 TATGAAATTTTGATAACCTCCCCATGAAATTTCGATATTGTCCC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACGTCTC
* * *
22660 TATAAAATTTTAATAACCACACTATGAAATTTTGATAACGTCTG
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACGTCTC
* ** *
22704 TATGAAATTTTGGTAAGTACACTATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACGTCTC
* * ** * * * ** *
22748 TACGAAATTTCGATTGCCTC-CTTACG-AAGTTTGATTTCCTCT-
1 TATGAAATTTTGATAACCACAC-TATGAAATTTTGATAACGTCTC
* *
22790 TGATGAAATTTTGATAACTACACTAT-AAATTTT-AGTAACAT-TCC
1 T-ATGAAATTTTGATAACCACACTATGAAATTTTGA-TAACGTCT-C
* * * * * *
22834 TATGAAATTTT-ATTAA--TCTCTATGAAATTTTAATATCACAATATA
1 TATGAAATTTTGA-TAACCACACTATGAAATTTTGATA--AC-GTCTC
* * * *
22879 TATAAAAATTTTTGGTAACCA-ACCTATGAAATTTTGGTAACCTC-C
1 TAT-GAAA-TTTTGATAACCACA-CTATGAAATTTTGATAACGTCTC
* * ** **
22924 GTATGAAATTGTGGTAATCTTCAC-ATGAAATTTTGATAACCACAT-
1 -TATGAAATTTTGATAA-CCACACTATGAAATTTTGATAACGTC-TC
** * * *
22969 TATGAAATTTTGATAACTTTC-TTATGAAACTTTGATTATATCTTCTC
1 TATGAAATTTTGATAAC-CACACTATGAAATTTTGA-TA-A-CGTCTC
* * *
23016 -ATGAAATTTTGATAACCACACCAT-AAAATTTGAATAACGCCTC
1 TATGAAATTTTGATAACCACACTATGAAATTTTG-ATAACGTCTC
* *
23059 TATGAAATTTTGATAACCACAC--TGAAATTTTAATAACCT-TC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACGTCTC
* * * *
23100 TAATG-AATTTCGGTAACTACACTATGAAATTTTGATAATTGTC-C
1 T-ATGAAATTTTGATAACCACACTATGAAATTTTGATAA-CGTCTC
* * * ** *
23144 TATGAAATTTTTG-TAATCATA-TCATGAAATTTTGACAACCACAC
1 TATGAAA-TTTTGATAACCACACT-ATGAAATTTTGATAACGTCTC
* * ** * *
23188 TGTGAAATTGTGATAACTTTC-TTATGAAATTTTGATAA--TATGC
1 TATGAAATTTTGATAAC-CACACTATGAAATTTTGATAACGTCT-C
*
23231 TATGAAATTTTGATAACTACACTACGGATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC--CAC-AC-TATGAAATTTTGATAAC
23274 TACACGGAAA
Statistics
Matches: 455, Mismatches: 106, Indels: 102
0.69 0.16 0.15
Matches are distributed among these distances:
41 22 0.05
42 22 0.05
43 100 0.22
44 214 0.47
45 27 0.06
46 30 0.07
47 26 0.06
49 14 0.03
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACTATGAAATTTTGATAACGTCTC
Found at i:22828 original size:21 final size:23
Alignment explanation
Indices: 22792--22845 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
22782 TTTCCTCTTG
22792 ATGAAATTTT-GATAAC-TACACT
1 ATGAAATTTTAGATAACATAC-CT
*
22814 AT-AAATTTTAG-TAACATTCCT
1 ATGAAATTTTAGATAACATACCT
22835 ATGAAATTTTA
1 ATGAAATTTTA
22846 TTAATCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (23 bp):
ATGAAATTTTAGATAACATACCT
Found at i:23063 original size:68 final size:68
Alignment explanation
Indices: 22940--23072 Score: 171
Period size: 68 Copynumber: 2.0 Consensus size: 68
22930 AATTGTGGTA
** * **
22940 ATCTTCACATGAAATTTTGATAACCACATTATGAAATTTTGATAACTTTCTTATGAAACTTTGAT
1 ATCTTCACATGAAATTTTGATAACCACACCATGAAAATTTGATAACCCTCTTATGAAACTTTGAT
23005 TAT
66 TAT
* *
23008 ATCTTCTCATGAAATTTTGATAACCACACCAT-AAAATTTGAATAACGCCTC-TATGAAATTTTG
1 ATCTTCACATGAAATTTTGATAACCACACCATGAAAATTTG-ATAAC-CCTCTTATGAAACTTTG
23071 AT
64 AT
23073 AACCACACTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 7 0.12
68 47 0.84
69 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (68 bp):
ATCTTCACATGAAATTTTGATAACCACACCATGAAAATTTGATAACCCTCTTATGAAACTTTGAT
TAT
Found at i:24208 original size:21 final size:20
Alignment explanation
Indices: 24160--24202 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
24150 AATTCAAAAC
24160 AAAATAAAAACTACCCATCT
1 AAAATAAAAACTACCCATCT
*
24180 TAAATAAAAACTACCCAT-T
1 AAAATAAAAACTACCCATCT
24199 AAAA
1 AAAA
24203 GATAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAAAAACTACCCATCT
Done.